Periodically-driven quantum systems can exhibit a plethora of intriguing non-equilibrium phenomena, that can be analyzed using Floquet theory. Naturally, Floquet theory is employed to describe the dynamics of atoms interacting with intense laser fields. However, this semiclassical analysis can not account for quantum-optical phenomena that rely on the quantized nature of light. In this paper, we take a significant step to go beyond the semiclassical description of atom-photon coupled systems by unifying Floquet theory with quantum optics using the framework of Full-Counting Statistics. This is achieved by introducing counting fields that keep track of the photonic dynamics. This formalism, which is dubbed "Photon-resolved Floquet theory" (PRFT), is based on two-point tomographic measurements, instead of the two-point projective measurements used in standard Full-Counting Statistics. Strikingly, the PRFT predicts the generation of macroscopic light-matter entanglement when atoms interact with multi-frequency electromagnetic fields, thereby leading to complete decoherence of the atomic subsystem in the basis of the Floquet states. This decoherence occurs rapidly in the optical frequency regime, but is negligible in the radio frequency regime. Intriguingly, time crystals can act as good quantum memories even in the optical frequency regime. Our results thus pave the way for the design of efficient quantum memories and quantum operations. Finally, employing the PRFT, we propose a quantum communication protocol that can significantly outperform the state-of-art few-photon protocols by two orders of magnitude or better. The PRFT potentially leads to new insights in various Floquet settings including spectroscopy, thermodynamics, quantum metrology, and quantum simulations.